[Gmod-help] Help w/ Chado RPM Build
Brian O'Connor
briandoconnor at gmail.com
Fri Jan 9 20:08:58 EST 2009
Hey Scott,
I updated to BioPerl-1.5.9_2 manually following the directions at
bioperl.org and the problem persisted. Any other ideas?
I didn't see this on the gmod.org site but do you also distribute db
dumps of clean databases (e.g. the default schema and base ontologies
loaded)? I could use that to make my RPM.
--Brian
Scott Cain wrote:
> Hi Brian,
>
> Bioperl is almost certainly a problem. Nothing else jumps out at me
> at the moment; it's been a while since I've used Pg 7.4, but I don't
> think there is a problem there.
>
> Thanks for the info about the ontology links--I wasn't aware that they
> were broken.
>
> Scott
>
>
> On Fri, Jan 9, 2009 at 3:50 PM, Brian O'Connor <briandoconnor at gmail.com> wrote:
>> Hey Dave, Scott, et al.
>>
>> I'm trying to update the chado RPMs we're using in the Nelson lab from
>> version 0.003 to 1.0 of the schema (hopefully these will be ready for the
>> GMOD meeting too!). So I downloaded the 1.0 schema release and followed the
>> install readme to build it first by hand before updating the RPM spec file.
>> Everything worked OK until the ontology load step. First, two of the URLs
>> referenced in load/tt2/load.conf.tt2 were out of date. It looks like
>> SourceForge is now using the following URLs:
>>
>> *
>> http://obo.cvs.sourceforge.net/viewvc/*checkout*/obo/obo/ontology/OBO_REL/relationship.obo
>> *
>> http://obo.cvs.sourceforge.net/viewvc/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo
>>
>> And this doesn't appear to be fixed in cvs HEAD e.g.:
>> http://gmod.cvs.sourceforge.net/viewvc/*checkout*/gmod/schema/chado/load/tt2/load.conf.tt2
>>
>> Anyway, that's a minor problem. However when I tried to do a "make
>> ontologies" step I get the following error:
>>
>> ++++++++++++++++++++++++
>> ...
>> fetching files for Sequence Ontology
>> +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>> updated
>> loading...DBD::Pg::st execute failed: ERROR: null value in column
>> "cv_id" violates not-null constraint
>> [for Statement "INSERT INTO cvterm (dbxref_id) VALUES (?)" with
>> ParamValues: 1='2033'] at /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.pm line
>> 3314.
>> DBD::Pg::st execute failed: ERROR: null value in column "cv_id" violates
>> not-null constraint
>> [for Statement "INSERT INTO cvterm (dbxref_id) VALUES (?)" with
>> ParamValues: 1='2033'] at /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.pm line
>> 3314.
>> at /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.pm line 3324
>> DBIx::DBStag::insertrow('DBIx::DBStag=HASH(0x84ebd40)', 'cvterm',
>> 'HASH(0x8d01e70)', 'cvterm_id') called at
>> /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
>> line 1920
>> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
>> 'Data::Stag::StagImpl=ARRAY(0x8d6e3c4)') called at
>> /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
>> line 1333
>> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
>> 'Data::Stag::StagImpl=ARRAY(0x8d556f4)', 'HASH(0x8d28fa0)') called at
>> /usr/lib/perl5/site_perl/
>> .8.5/DBIx/DBStag.pm line 2077
>> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
>> 'Data::Stag::StagImpl=ARRAY(0x8d6b0dc)') called at
>> /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
>> line 1333
>> DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
>> 'Data::Stag::StagImpl=ARRAY(0x8d1ad5c)') called at
>> /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
>> line 1180
>> DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x84ebd40)',
>> 'Data::Stag::StagImpl=ARRAY(0x8d38e0c)') called at
>> /usr/bin/stag-storenode.pl line 88
>> eval {...} called at /usr/bin/stag-storenode.pl line 87
>> main::store('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
>> 'Data::Stag::StagImpl=ARRAY(0x8d38e0c)') called at
>> /usr/bin/stag-storenode.pl line 137
>> main::__ANON__('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
>> 'Data::Stag::StagImpl=ARRAY(0x8d38e0c)') called at
>> /usr/lib/perl5/site_perl/5.8.5/Data/Stag/Ba
>> eHandler.pm line 572
>>
>> Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
>> 'cvterm_relationship') called at /usr/lib/perl5/site_perl/5.8.5/Data/Stag/
>> aseHandler.pm line 720
>>
>> Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
>> 'HASH(0x8c810c8)') called at /usr/lib/perl5/vendor_perl/5.8.5/XML/Parser
>> PerlSAX.pm line 239
>>
>> XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x8c46ca0)',
>> 'XML::Parser::Expat=HASH(0x8727b64)', 'cvterm_relationship') called at
>> /usr/li
>> /perl5/vendor_perl/5.8.5/XML/Parser/PerlSAX.pm line 79
>>
>> XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x8727b64)',
>> 'cvterm_relationship') called at
>> /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread
>> multi/XML/Parser/Expat.pm line 469
>> XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x8727b64)',
>> 'FileHandle=GLOB(0x8c7e6e4)') called at
>> /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thre
>> d-multi/XML/Parser.pm line 187
>> eval {...} called at
>> /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi/XML/Parser.pm line
>> 186
>> XML::Parser::parse('XML::Parser=HASH(0x87272c4)',
>> 'FileHandle=GLOB(0x8c7e6e4)') called at
>> /usr/lib/perl5/vendor_perl/5.8.5/XML/Parser/PerlSAX.pm line 14
>>
>> XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x8c46ca0)',
>> 'Handler', 'Data::Stag::BaseHandler=HASH(0x8bb2cc8)', 'Source',
>> 'HASH(0x8c1dfa0)') c
>> lled at /usr/lib/perl5/site_perl/5.8.5/Data/Stag/XMLParser.pm line 69
>>
>> Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x8b31360)',
>> 'FileHandle=GLOB(0x8c7e6e4)') called at
>> /usr/lib/perl5/site_perl/5.8.5/Data/Sta
>> /BaseGenerator.pm line 476
>>
>> Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x8b31360)',
>> '-file', 'tmp/song/so.oboxml', '-str', 'undef', '-fh', 'undef') called at
>> /usr
>> lib/perl5/site_perl/5.8.5/Data/Stag/XMLParser.pm line 58
>>
>> Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x8b31360)',
>> '-file', 'tmp/song/so.oboxml', '-str', 'undef', '-fh', 'undef') called at
>> /usr/lib
>> perl5/site_perl/5.8.5/Data/Stag/StagImpl.pm line 259
>> Data::Stag::StagImpl::parse('Data::Stag', '-format', 'undef',
>> '-file', 'tmp/song/so.oboxml', '-handler',
>> 'Data::Stag::BaseHandler=HASH(0x8bb2cc8)') call
>> d at /usr/lib/perl5/site_perl/5.8.5/Data/Stag.pm line 179
>> Data::Stag::AUTOLOAD('Data::Stag', '-format', 'undef', '-file',
>> 'tmp/song/so.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x8bb2cc8)')
>> called at /
>> sr/bin/stag-storenode.pl line 143
>> System call 'stag-storenode.pl -d
>> 'dbi:Pg:dbname=chado_v_1.0;host=localhost;port=5432' --user gmod
>> tmp/song/so.oboxml' failed: 256
>> Died at /home/gmod/Dev/gmod-1.0/lib/Chado/Builder.pm line 315, <STDIN> line
>> 1.
>> make: *** [ontologies] Error 2
>> ++++++++++++++++++++++++
>>
>> I'm using the following RPMs, see any dependency issues?
>>
>> httpd-2.0.52-32.ent.centos4
>> perl-bioperl-1.5-1.9.bp.centos4 (may need > 1.5.2?)
>> perl-go-perl-0.02-4.bp.centos4
>> postgresql-server-7.4.17-1.RHEL4.1
>> ant (missing)
>> perl-DBI-1.47-1.8.bp.centos4
>> perl-DBD-Pg-1.49-1.9.bp.centos4
>> perl-SQL-Translator-0.07-1.4.bp.centos4
>> perl-Data-Stag-0.08-1.12.bp.centos4
>> perl-XML-Parser-2.34-5
>> perl-Module-Build-0.25-1.3.bp.centos4
>> perl-Class-DBI-0.96-1.4.bp.centos4
>> perl-Class-DBI-Pg-0.08-1.7.bp.centos4
>> perl-Class-DBI-Pager-0.06-1.5.bp.centos4
>> perl-DBIx-DBStag-0.07-1.5.bp.centos4 (manually updated to DBIx-DBStag-0.10
>> and dep of DBIx-DBSchema-0.36)
>> perl-XML-Simple-2.14-1.3.bp.centos4
>> perl-libwww-perl-5.805-1.12.bp.centos4
>> perl-Template-Toolkit-2.14-1.9.bp.centos4
>> perl-Log-Log4perl-0.51-1.5.bp.centos4
>>
>> Any ideas? Sorry if there's something obvious that I'm doing wrong, I
>> haven't built a DB from scratch in a long time :-)
>>
>> Thanks for the help.
>>
>> --Brian
>>
>
>
>
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